Kelly L. Sovacool

Bioinformatician building and applying open source tools for microbiome research
Contributing to data science education along the way

Contact:   sovacool [at] umich.edu

View a PDF version of my CV:   https://sovacool.dev/latex-cv/cv_KLS.pdf

Education

Dates Degree Institution
2018-present PhD Bioinformatics University of Michigan, Dept. of Computational Medicine and Bioinformatics
Advisor: Patrick D. Schloss
2014-2018 BS Biology University of Kentucky, Dept. of Biology
Minor: Computer Science
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Research Experience

Dates Title Lab Projects
2019-present Graduate Student Researcher Schloss Lab, Dept. of Microbiology and Immunology,
University of Michigan
  • Develop and benchmark bioinformatics pipelines and software for microbial ecology.
  • Analyze 16S rRNA gene amplicon sequence data.
  • Apply machine learning methods to gut microbiome classification problems in colorectal cancer and C. difficile infection.
  • Collaborate with other scientists on microbiome projects and mentor junior lab members.
2018-2019 Rotation Student Researcher Program in Biomedical Sciences,
University of Michigan
2015-2018 Undergraduate Lab Assistant Moseley Bioinformatics Lab, Dept. of Molecular and Cellular Biochemistry,
University of Kentucky
  • Developed a computational tool in Python for identifying sets of orthologous and paralogous gene products in whole genomes to facilitate collinearity analysis and detection of gene duplication events.
2016-2018 BIO395 Independent Research Student Weisrock Lab, Dept. of Biology,
University of Kentucky
  • Developed bash scripts and a SNP calling pipeline in Snakemake.
  • Population structure analysis of the Ambystoma tigrinum species complex.
  • Bayesian species delimitation of the Desmognathus fuscus species complex.
2015-2016 Undergraduate Lab Assistant Jaromczyk Lab, Dept. of Computer Science,
University of Kentucky
  • Maintained the Epichloë festucae genome project database.
  • Analyzed RNA-seq data of Chenopodium quinoa and coffee ringspot virus.
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Service

Dates Title Organization Projects
2019-present Executive Committee Member: Open Source Technical Lead Girls Who Code at U-M DCMB
  • Plan, apply for funding, develop curriculum, and maintain resources to teach introductory Python programming & data science to young women+.
  • Facilitate collaborative development and maintenance of our open source teaching resources.
  • Organize our year-round Club and annual Data Science Summer Experience for high school women+.
2019-present Organizer & Maintainer U-M Carpentries
  • Co-lead development & maintenance of a curriculum for workshops teaching programming skills for reproducible research.
  • Maintain the website, develop curriculum, and organize workshops.
  • Collaborate with U-M Women in Science and Engineering to organize workshops for women+.
2021-present Mentor Schloss Lab Mentor an undergraduate student in building reproducible machine learning models to predict C. difficile infection severity from gut microbiome composition.
2021-present CoderSpaces co-host U-M ISR Data Science Hub Hold office hours at a weekly virtual help session for data science practitioners
2021-present Peer reviewer PLOS ONE (1)
2019-2021 Graduate Student Coordinator U-M Data Analysis Networking Group
  • Organize monthly meetings & a one-day symposium for researchers to sharpen their data analysis skills.
  • Apply for funding through a Rackham Interdisciplinary Workshop grant.
2009-present Volunteer Sound Engineer various churches and non-profit organizations
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Teaching Experience

dates Title Organization Event(s)
Jan-Apr 2023 Graduate Student Instructor Dept. of Computational Medicine & Bioinformatics BIOINF 576: Tool Development for Bioinformatics
2019-2022 Facilitator & Capstone Project Mentor Girls Who Code at U-M DCMB Weekly Club during the school year and week-long Summer Experience for high schoolers to learn Python for data science
2018-present Workshop Instructor & Helper U-M Carpentries 2-day Software Carpentry workshops teaching computational skills for reproducible research
Jun 2022 Instructor Intro to R & RNA-Seq Workshop for ASM Microbe conference attendees
Apr 2019 DNA Day Ambassador Michigan DNA Day Epigenetics & Scientific Journeys
Mar 2019 Workshop helper Graduate Society of Black Engineers and Scientists Data Visualization with Python Workshop
Mar 2019 Capstone Activity Leader Females Excelling More in Math, Engineering, & the Sciences Binary Numbers through Ozobots with GWC at U-M DCMB
2012-2018 Tutor freelance for high school and college students in Biology, Calculus, Chemistry, Computer Science, and Bioinformatics.
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Continuing Education

Date Title Organization Location
Jan 2020 Building Tidy Tools workshop at rstudio::conf Rstudio, PBC San Francisco, CA
Dec 2019 Winter School in Research Software Engineering US Research Software Sustainability Institute Seattle, WA
Jun 2019 Software Carpentry Instructor Training The Carpentries University of Michigan
May 2019 PyCon Education Summit & Conference The Python Software Foundation Cleveland, OH
Apr 2019 MICROBIOL 612.2 Riffomonas Minimal R Workshop University of Michigan
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Awards

Grants

Dates Title Institution Amount
2022 Conference Travel Grant Rackham Graduate School
University of Michigan 		$900
2020-2021 Rackham Interdisciplinary Workshop Grant Rackham Graduate School
University of Michigan 		$500
2020 Conference Travel Grant Rackham Graduate School
University of Michigan 		$800
2019-2020 Rackham Interdisciplinary Workshop Grant Rackham Graduate School
University of Michigan 		$500
2019-2021 NIH T32 Bioinformatics Training Program Fellow Bioinformatics Graduate Program
University of Michigan
2017 Oswald Research & Creativity Award
2nd place in Biological Sciences 		Office of Undergraduate Research
University of Kentucky 		$200
2017 Summer Research Grant Office of Undergraduate Research
University of Kentucky 		$2,000
2014-2018 Presidential Scholarship University of Kentucky out-of-state full tuition
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Honors

Dates Title Institution
2018 Graduated Cum Laude with Departmental Honors in Biology University of Kentucky
2018 Biology Undergraduate Research Award Nominee University of Kentucky
2014-2018 Lewis Honors College University of Kentucky
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Publications

Last updated: December 08, 2022

* Indicates co-first author.

Date Article Authors badges
2022 Sep Streamlined implementation of a machine learning model to classify screen relevant neoplasia using reference-based OTU clustering. bioRxiv Armour CR, Sovacool KL, Close WL, Topçuoğlu BD, Wiens J, Schloss PD
2022 Jul Intestinal Inflammation Reversibly Alters the Microbiota to Drive Susceptibility to Clostridioides Difficile Colonization in a Mouse Model of Colitis. mBio Barron MR, Sovacool KL, Abernathy-Close L, Vendrov KC, Standke AK, Bergin IL, Schloss PD, Young VB
2022 Feb OptiFit: An Improved Method for Fitting Amplicon Sequences to Existing OTUs. mSphere Sovacool KL, Westcott SL, Mumphrey MB, Dotson GA, Schloss PD
2022 Jan Developing and Deploying an Integrated Workshop Curriculum Teaching Computational Skills for Reproducible Research. JOSE *Lapp Z, *Sovacool KL, Lesniak N, King D, Barnier C, Flickinger M, Krüger J, Armour CR, Lapp MM, Tallant J, Diao R, Oneka M, Tomkovich S, Anderson JM, Lucas SK, Schloss PD
2021 Dec Teaching Python for Data Science: Collaborative Development of a Modular & Interactive Curriculum. JOSE *Duda M, *Sovacool KL, Farzaneh N, Nguyen VK, Haynes SE, Falk H, Furman KL, Walker LA, Diao R, Oneka M, Drotos AC, Woloshin A, Dotson GA, Kriebel A, Meng L, Thiede SN, Lapp Z, Wolford BN
2021 May Mikropml: User-Friendly R Package for Supervised Machine Learning Pipelines. JOSS *Topçuoğlu BD, *Lapp Z, *Sovacool KL, Snitkin E, Wiens J, Schloss PD
2021 Apr Geography Is More Important than Life History in the Recent Diversification of the Tiger Salamander Complex. PNAS Everson KM, Gray LN, Jones AG, Lawrence NM, Foley ME, Sovacool KL, Kratovil JD, Hotaling S, Hime PM, Storfer A, Parra-Olea G, Percino-Daniel R, Aguilar-Miguel X, O’Neill EM, Zambrano L, Shaffer HB, Weisrock DW
2020 Aug Ten Simple Rules to Increase Computational Skills among Biologists with Code Clubs. PLoS Comput Biol Hagan AK, Lesniak NA, Balunas MJ, Bishop L, Close WL, Doherty MD, Elmore AG, Flynn KJ, Hannigan GD, Koumpouras CC, Jenior ML, Kozik AJ, McBride K, Rifkin SB, Stough J, Sovacool KL, Sze MA, Tomkovich S, Topcuoglu BD, Schloss PD
2016 Aug Processing RNA-Seq Data of Plants Infected with Coffee Ringspot Virus. BMC Bioinform Goodin MM, Farman M, Inocencio H, Jang C, Jaromczyk JW, Moore N, Sovacool KL
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Presentations

Talks

Date Event Title Location
Nov 2022 Bioinformatics Student Research Hour Predicting C. difficile infection severity from the taxonomic composition of the gut microbiome University of Michigan
Feb 2022 Seminar for the KG Jebsen Center for Genetic Epidemiology Intro to git & GitHub (Virtual) Norwegian University of Science and Technology
Mar 2021 Bioinformatics Student Research Hour OptiFit: a fast method for fitting amplicon sequences to existing OTUs (Virtual) University of Michigan
Apr 2018 Systems Biology and Omics Integration Seminar Developing a Global Homology Analysis for Comparative Genomics University of Kentucky
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Posters

Date Event Title Location
Jun 2022 ASM Microbe Predicting the severity of C. difficile infections from the taxonomic composition of the gut microbiome Washington, DC
Jun 2020 ASM Microbe OptiFit: a fast method for fitting amplicon sequences to existing OTUs Virtual
Apr 2018 Showcase for Undergraduate Scholars Developing a Global Homology Analysis for Comparative Genomics University of Kentucky
Apr 2018 National Conference on Undergraduate Research Developing a Global Homology Analysis for Comparative Genomics University of Central Oklahoma
Apr 2016 Showcase for Undergraduate Scholars Processing RNA-seq Reads of Plants Infected with the Coffee Ringspot Virus University of Kentucky
Apr 2016 UT-KBRIN Bioinformatics Summit Processing RNA-seq Reads of Plants Infected with the Coffee Ringspot Virus Cadiz, KY
Apr 2015 Showcase for Undergraduate Scholars The Effect of Meditation on Performance University of Kentucky
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Open Source Contributions

Skills